2WLQ

Nucleophile-disabled Lam16A mutant holds laminariheptaose (L7) in a cyclical conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Synthesis of Cyclic Beta-Glucan Using Laminarinase 16A Glycosynthase Mutant from the Basidiomycete Phanerochaete Chrysosporium.

Vasur, J.Kawai, R.Jonsson, K.H.Widmalm, G.Engstrom, A.Frank, M.Andersson, E.Hansson, H.Forsberg, Z.Igarashi, K.Samejima, M.Sandgren, M.Stahlberg, J.

(2010) J.Am.Chem.Soc. 132: 1724

  • DOI: 10.1021/ja909129b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosynthases are precise molecular instruments for making specifically linked oligosaccharides. X-ray crystallography screening of ligands bound to the 1,3(4)-beta-D-glucanase nucleophile mutant E115S of Phanerochaete chrysosporium Laminarinase 16A ...

    Glycosynthases are precise molecular instruments for making specifically linked oligosaccharides. X-ray crystallography screening of ligands bound to the 1,3(4)-beta-D-glucanase nucleophile mutant E115S of Phanerochaete chrysosporium Laminarinase 16A (Lam16A) showed that laminariheptaose (L7) bound in an arch with the reducing and nonreducing ends occupying either side of the catalytic cleft of the enzyme. The X-ray structure of Lam16A E115S in complex with alpha-laminariheptaosyl fluoride (alphaL7F) revealed how alphaL7F could make a nucleophilic attack upon itself. Indeed, when Lam16A E115S was allowed to react with alphaL7F the major product was a cyclic beta-1,3-heptaglucan, as shown by mass spectrometry. NMR confirmed uniquely beta-1,3-linkages and no reducing end. Molecular dynamics simulations indicate that the cyclic laminariheptaose molecule is not completely planar and that torsion angles at the glycosidic linkages fluctuate between two energy minima. This is the first report of a glycosynthase that joins the reducing and nonreducing ends of a single oligosaccharide and the first reported synthesis of cyclic beta-glucan.


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, POB 590, SE-754 21 Uppsala, Sweden. jonas.vasur@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE LAMINARINASE
A
298Phanerochaete chrysosporiumMutation(s): 1 
Gene Names: lam16A
Find proteins for Q874E3 (Phanerochaete chrysosporium)
Go to UniProtKB:  Q874E3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.273α = 90.00
b = 47.910β = 90.00
c = 152.400γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
SCALAphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-09-21
    Type: Database references, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2017-07-12
    Type: Advisory, Data collection, Derived calculations
  • Version 2.0: 2017-11-08
    Type: Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-05-08
    Type: Data collection, Experimental preparation